The issue can be reproduced on the Plotly website itself. Navigate to https://plot.ly/javascript/custom-buttons/#update-button
When you hover over the chart, you can view the modebar.

When you click on any button, the modebar disappears.

Thanks for reporting!
The report feels similar to https://github.com/plotly/plotly.js/issues/3809
This is probably a side-effect of #3589
I know the issue is closed, but it happens the same when using restyle method, which can be seen in the demos online (https://plotly.com/javascript/custom-buttons/). I was wondering if that can also be fixed?
Most helpful comment
I know the issue is closed, but it happens the same when using restyle method, which can be seen in the demos online (https://plotly.com/javascript/custom-buttons/). I was wondering if that can also be fixed?